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16s rRNA Sequencing with MR DNA

16S ribosomal  (rRNA) sequencing using next generation sequencing is a method used to identify and compare bacteria and archaea present within almost any type of sample. 16S rRNA gene sequencing is a well-established method for studying phylogeny and taxonomy of samples from complex microbiomes or environments that are difficult or impossible to study.

 

 

 

 

16s sequencing illumina or PGM low cost prices with MR DNA

MR DNA is a next generation sequencing provider with low cost 16s sequencing services.

 

 

   enom Data. 2016 Jan 16;7:222-5. doi: 10.1016/j.gdata.2016.01.011. eCollection 2016.

Investigation of the microbial community in the Odisha hot spring cluster based on the cultivation independent approach.

Singh A1, Subudhi E1, Sahoo RK1, Gaur M1.

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Abstract

Deulajhari hot spring is located in the Angul district of Odisha. The significance of this hot spring is the presence of the hot spring cluster adjacent to the cold spring which attracts the attention of microbiologists to understand the role of physio-chemical factors of these springs on bacterial community structure. Next-generation sequencing technology helps us to depict the pioneering microflora of any ecological niche based on metagenomic approach. Our study represents the first Illumina based metagenomic study of Deulajhari hot spring DH1, and DH2 of the cluster with temperature 65 °C to 55 °C respectively establishing a difference of 10 °C. Comprehensive study of microbiota of these two hot springs was done using the metagenomic sequencing of 16S rRNA of V3-V4 region extracting metagenomic DNA from the two hot spring sediments. Sequencing community DNA reported about 28 phyla in spring DH1 of which the majority were Chloroflexi (22.98%), Proteobacteria (15.51%), Acidobacteria (14.51%), Chlorobi (9.52%), Nitrospirae (8.54%), and Armatimonadetes (7.07%), at the existing physiochemical conditions like; temperature 65 °C, pH 8.06, electro conductivity 0.020 dSm(- 1), and total organic carbon (TOC) 3.76%. About 40 phyla were detected in cluster DH2 at the existing physiochemical parameters like temperature 55 °C, pH 8.10, electro conductivity 0.019 dSm(- 1), and total organic carbon (TOC) 0.58% predominated with Chloroflexi (41.98%), Proteobacteria (10.74%), Nitrospirae (10.01%), Chlorobi (8.73%), Acidobacteria (6.73%) and Planctomycetes (3.73%). Approximately 68 class, 107 order, 171 genus and 184 species were reported in cluster DH1 but 102 class, 180 order, 375 genus and 411 species in cluster DH2. The comparative metagenomics study of the Deulajhari hot spring clusters DH1, and DH2 depicts the differential profile of the microbiota. Metagenome sequences of these two hot spring clusters are deposited to the SRA database and are available in NCBI with accession no. SRX1459734 for DH1 and SRX1459735 for DH2.

KEYWORDS:

16S rRNA; Deulajhari; Metagenomics; Next-generation sequencing

PMID: 26981412 PMCID: PMC4778664 DOI: 10.1016/j.gdata.2016.01.011

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7.

Genom Data. 2016 Jan 7;7:187-8. doi: 10.1016/j.gdata.2016.01.004. eCollection 2016.

Profiling of microbial community of Odisha hot spring based on metagenomic sequencing.

Singh A1, Subudhi E1.

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Abstract

Deulajhari hot spring has diverse temperature and pH range varying from 43 °C to 65 °C and 7.83 to 8.10 respectively. Dense foliage around Deulajhari hot spring contributes to the high total organic carbon content (TOC). In our experiment we took sediment samples from the two Deulajhari hot springs (S1 and S2) out of the cluster having temperature of 43 °C and 55 °C and pH of 7.83 and 7.14 respectively. Sediment samples were analysed using 16S rRNA of V3-V4 region by amplicon metagenome sequencing. Over 34 phyla were detected in cluster S1 and 32 phyla in cluster S2 at the existing physiochemical parameters temperature 43 °C, pH 7.83, electroconductivity 0.019 dSm(- 1), and total organic carbon (TOC) 3.80% for S1 and temperature 55 °C, pH 7.14, electroconductivity 0.019 dSm(- 1), and total organic carbon (TOC) 0.97% for S2. Existence of a vast number of unresolved sequences 179 out of 292 in S1 and 186 out of 314 in S2 at the genus level emphasizes the significance of our study. Metagenome sequence information for the both clusters S1 and S2 of Deulajhari is available at NCBI, SRA database with accession number SRX1459732 and SRX1459733 respectively. Direct link to the deposited data: www.ncbi.nlm.nih.gov/sra/SRX1459732 www.ncbi.nlm.nih.gov/sra/SRX1459733.

KEYWORDS:

16S rRNA; Deulajhari; Illumina platform; Metagenome; TOC

PMID: 26981405 PMCID: PMC4778635 DOI: 10.1016/j.gdata.2016.01.004

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8.

Genom Data. 2015 Dec 28;7:127-8. doi: 10.1016/j.gdata.2015.12.019. eCollection 2016.

Cultivation-independent comprehensive investigations on bacterial communities in serofluid dish, a traditional Chinese fermented food.

Chen P1, Wu Z1, Zhao Y2, Wei Y2, Xu R1, Yan L3, Li H1.

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Abstract

Serofluid dish (or Jiangshui, in Chinese), a traditional food in the Chinese culture, is made from vegetables by fermentation. In this study, bacterial community of the fermented serofluid dish was assessed by Illumina amplicon sequencing. The metagenome comprised of 49,589 average raw reads with an average 11,497,917 bp and G + C content is 52.46%. This is the first report on V4 hyper-variable region of the 16S rRNA metagenome sequence employing Illumina platform to profile the microbial community of this little known fermented food from Gansu Province, China. The metagenome sequence can be accessed at NCBI, SRA database accession no. SRP065370.

KEYWORDS:

16S rRNA; Cultivation-independent; Jiangshui; Microbial diversity; Serofluid dish

PMID: 26981386 PMCID: PMC4778640 DOI: 10.1016/j.gdata.2015.12.019

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9.

Genom Data. 2015 Dec 18;7:101-2. doi: 10.1016/j.gdata.2015.12.004. eCollection 2016.

Structural insights of microbial community of Deulajhari (India) hot spring using 16s-rRNA based metagenomic sequencing.

Singh A1, Subudhi E1.

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Abstract

Insights about the distribution of the microbial community prove to be the major goal of understanding microbial ecology which remains to be fully deciphered. Hot springs being hub for the thermophilic microbiota attract the attention of the microbiologists. Deulajhari hot spring cluster is located in the Angul district of Odisha. Covered within a wooded area, Deulajhari hot spring is also fed by the plant litter resulting in a relatively high amount of total organic content (TOC). For the first time, Illumina sequencing based biodiversity analysis of microbial composition is studied through amplicon metagenome sequencing of 16s rRNA targeting V3-V4 region using metagenomic DNA from the hot spring sediment. Over 28 phyla were detected through the amplicon metagenome sequencing of which the most dominating phyla at the existing physiochemical parameters like; temperature 69 °C, pH 8.09, electroconductivity 0.025 dSm(- 1) and total organic carbon 0.356%, were Proteobacteria (88.12%), Bacteriodetes (10.76%), Firmicutes (0.35%), Spirochetes (0.18%) and chloroflexi (0.11%). Approximately 713 species were observed at the above physiochemical parameters. The analysis of the metagenome provides the quantitative insights into microbial populations based on the sequence data in Deulajhari hot spring. Metagenome sequence is deposited to SRA database which is available at NCBI with accession no. SRX1459736.

KEYWORDS:

16s rRNA; Deulajhari hot spring; Illumina sequencing; TOC

PMID: 26981376 PMCID: PMC4778618 DOI: 10.1016/j.gdata.2015.12.004

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17.

Colorectal Dis. 2016 Sep 27. doi: 10.1111/codi.13534. [Epub ahead of print]

A collaborative study of the current concepts and challenges for treatment of anastomotic leakage in colorectal surgery.

Vallance A1,2, Wexner S3, Berho M4, Cahill R5, Coleman M6, Haboubi N7, Heald RJ8, Kennedy RH9, Moran B8, Mortensen N2, Motson RW10, Novell R11, O'Connell PR5, Ris F12, Rockall T13, Senapati A14, Windsor A15, Jayne DG16.

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Abstract

The reduction of the incidence, detection, and treatment of anastomotic leakage (AL) continues to challenge the colorectal surgical community. AL is not consistently defined and reported in clinical studies, its occurrence is variably reported and its impact on long-term morbidity and healthcare resources has received relatively little attention. Controversy continues about the best strategies to reduce the risk. Diagnostic tests lack sensitivity and specificity, resulting in delayed diagnosis and increased morbidity. Intraoperative fluorescence angiography has recently been introduced as a means of real-time assessment of anastomotic perfusion with preliminary evidence suggesting that it may reduce the rate of AL. In addition, concepts are emerging about the role of the rectal mucosal microbiome in AL and the possible role of new prophylactic therapies. In January 2016 a meeting of expert colorectal surgeons and pathologists was held in London, UK to identify the ongoing controversies surrounding AL in colorectal surgery. The outcome of the meeting is presented in the form of research challenges that need to be addressed. This article is protected by copyright. All rights reserved.

This article is protected by copyright. All rights reserved.

PMID: 27671222 DOI: 10.1111/codi.13534

 

16s rRNA Sequencing with MR DNA

16S ribosomal  (rRNA) sequencing using next generation sequencing is a method used to identify and compare bacteria and archaea present within almost any type of sample. 16S rRNA gene sequencing is a well-established method for studying phylogeny and taxonomy of samples from complex microbiomes or environments that are difficult or impossible to study.

 

 

 

 

16s sequencing illumina or PGM low cost prices with MR DNA

MR DNA is a next generation sequencing provider with low cost 16s sequencing services.

Select item 27670882

 

19.

Sci Rep. 2016 Sep 27;6:33965. doi: 10.1038/srep33965.

Probiotic legacy effects on gut microbial assembly in tilapia larvae.

Giatsis C1, Sipkema D2, Ramiro-Garcia J2,3,4, Bacanu GM2, Abernathy J5, Verreth J1, Smidt H2, Verdegem M1.

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Abstract

The exposure of fish to environmental free-living microbes and its effect on early colonization in the gut have been studied in recent years. However, little is known regarding how the host and environment interact to shape gut communities during early life. Here, we tested whether the early microbial exposure of tilapia larvae affects the gut microbiota at later life stages. The experimental period was divided into three stages: axenic, probiotic and active suspension. Axenic tilapia larvae were reared either under conventional conditions (active suspension systems) or exposed to a single strain probiotic (Bacillus subtilis) added to the water. Microbial characterization by Illumina HiSeq sequencing of 16S rRNA gene amplicons showed the presence of B. subtilis in the gut during the seven days of probiotic application. Although B. subtilis was no longer detected in the guts of fish exposed to the probiotic after day 7, gut microbiota of the exposed tilapia larvae remained significantly different from that of the control treatment. Compared with the control, fish gut microbiota under probiotic treatment was less affected by spatial differences resulting from tank replication, suggesting that the early probiotic contact contributed to the subsequent observation of low inter-individual variation.

PMID: 27670882 DOI: 10.1038/srep33965

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20.

Mol Nutr Food Res. 2016 Sep 27. doi: 10.1002/mnfr.201600552. [Epub ahead of print]

Reduction in cardiometabolic risk factors by a multifunctional diet is mediated via several branches of metabolism as evidenced by non-targeted metabolite profiling approach.

Tovar J1, de Mello VD2, Nilsson A3, Johansson M3, Paananen J2, Lehtonen M4, Hanhineva K2, Björck I3.

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Abstract

SCOPE:

MFD, a diet based on multiple functional concepts and ingredients with antiinflammatory activity, was previously shown to improve different cardiometabolic risk-associated markers in healthy subjects. Here, we assessed the impact of MFD on plasma metabolome and explored associations of the differential metabolites with clinical parameters, searching for metabolic determinants related to the effects of MFD.

METHODS AND RESULTS:

Forty-four overweight healthy volunteers completed a randomized crossover intervention comparing MFD with a control diet devoid of the active components of MFD. Fasting plasma samples were analyzed with non-targeted metabolite profiling at baseline and at the end (4 wk) of each diet period by liquid chromatography coupled to quadrupole-time of flight-MS system, revealing a vast impact of MFD on metabolic homeostasis. Main metabolite classes affected included acylcarnitines, furan fatty acids, phospholipids (plasmalogens, phosphatidylcholines, phosphatidylethanolamines), and various low-molecular weight products from the bioactivity of gut microbiota. Circulating levels of several of these metabolites correlated with changes in clinical blood lipid biomarkers.

CONCLUSIONS:

The metabolomics approach revealed that consumption of MFD affected different areas of metabolism, highlighting the impact of a healthy diet on plasma metabolome. This seems linked to reduced cardiometabolic risk and provides mechanistic insight into the effects of MFD. This article is protected by copyright. All rights reserved.

This article is protected by copyright. All rights reserved.

KEYWORDS:

Cardiometabolic diseases; Dietary prevention; Functional foods; Metabolic syndrome; Plasma metabolomics

PMID: 27670644 DOI: 10.1002/mnfr.201600552

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16s rRNA Sequencing with MR DNA

16S ribosomal  (rRNA) sequencing using next generation sequencing is a method used to identify and compare bacteria and archaea present within almost any type of sample. 16S rRNA gene sequencing is a well-established method for studying phylogeny and taxonomy of samples from complex microbiomes or environments that are difficult or impossible to study.

 

 

 

 

16s sequencing illumina or PGM low cost prices with MR DNA

MR DNA is a next generation sequencing provider with low cost 16s sequencing services.

 

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